Automatically determining cause of death from verbal autopsy narratives

BACKGROUND: A verbal autopsy (VA) is a post-hoc written interview report of the symptoms preceding a person’s death in cases where no official cause of death (CoD) was determined by a physician. Current leading automated VA coding methods primarily use structured data from VAs to assign a CoD category. We present a method to automatically determine CoD categories from VA free-text narratives alone. METHODS: After preprocessing and spelling correction, our method extracts word frequency counts from the narratives and uses them as input to four different machine learning classifiers: naïve Bayes, random forest, support vector machines, and a neural network. RESULTS: For individual CoD classification, our best classifier achieves a sensitivity of.770 for adult deaths for 15 CoD categories (as compared to the current best reported sensitivity of.57), and.662 with 48 WHO categories. When predicting the CoD distribution at the population level, our best classifier achieves.962 cause-specific mortality fraction accuracy for 15 categories and.908 for 48 categories, which is on par with leading CoD distribution estimation methods. CONCLUSIONS: Our narrative-based machine learning classifier performs as well as classifiers based on structured data at the individual level. Moreover, our method demonstrates that VA narratives provide important information that can be used by a machine learning system for automated CoD classification. Unlike the structured questionnaire-based methods, this method can be applied to any verbal autopsy dataset, regardless of the collection process or country of origin. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12911-019-0841-9) contains supplementary material, which is available to authorized users.